Fig. 7. sciMAP-ATAC applied to a mouse model of ischemic injury.

a Experimental design using a mouse MCAO model of ischemic injury. Mice were sacrificed 3 days post surgery (dps) and brains flash-frozen in TFM. Alternating thin (20 µm) and thick (200 µm) sections were processed using IHC to define infarction (red outline) and peri-infarct area (pink outline) and sciMAP-ATAC punching schematic, respectively. b GFAP IHC of a 20 µm coronal section of an ischemic mouse brain. Punch positions along the 5–8 axis (core-to-border) are indicated. Background corrected GFAP fluorescence along the 5–8 axis is shown to the right for stroke and contralateral hemispheres (n = 10). Data are presented as linear fitted model ± SEM; boxplot center line represents median, lower and upper hinges represent first and third quartiles, and whiskers extend from hinge to ±1.5 × IQR, (scale bar, 1 mm) c. UMAP of cells colored by the three conditions. d UMAP as in c, colored by clusters assigned to cell type (Olig oligodendrocytes, Astro astrocytes, Micro/MΦ microglia/macrophage, GABA GABAergic (inhibitory) neurons, Glut glutamatergic (excitatory) neurons). e Cell × topic matrix colored by normalized topic weights, as in c, d and annotated by conditions and cell type as given at the bottom reveals substantially divergent topic weighting in cells from the stroke punches (left). Topic 30, enriched specifically in the stroke cells belonging to the chromatin-disrupted cluster, has peaks enriched for ontologies associated with ischemic injury with reperfusion. Colored by −log₁₀ false discovery rate (FDR) Q-value, height by log₂ fold enrichment (right). Source data are provided as a Source data file.